He took part in the staged Gleiwitz incident, a false flag operation intended to provide the justification for the attack on Poland by Nazi Germany, which ultimately culminated in starting World War II.

[4] On 10 August 1939, Reinhard Heydrich informed Naujocks of his mission to lead a small group of German operatives to seize the Gleiwitz radio station.

[9] More recently, author and researcher Jak Mallmann Showell's investigation has suggested that Naujocks' claims as to his actions at the Gleiwitz radio station may have been a fabrication to curry special handling by the Allies after the war.

[11] Later, on 9 November 1939, Naujocks (along with Walter Schellenberg) participated in the Venlo incident, which saw the capture in the Netherlands of two British SIS agents, Captain Sigismund Payne Best and Major Richard Henry Stevens.

In 1943, due to ill health, he was sent to the West, where he served as an economic administrator the following year for German troops in Belgium, while involving himself in the deaths of several Belgian underground and Danish resistance members.

[3] After his promotion to Obersturmführer (first lieutenant) he participated in sabotage and terrorist actions against the Danish population from December 1943 until autumn 1944, as the leader of the "Peter Group", including the murder of Lutheran pastor Kaj Munk.

[3] At the Nuremberg Trials, Naujocks declared the attack against the Gleiwitz radio tower was under orders from Heinrich Müller, the head of Gestapo and his superior, Reinhard Heydrich.